› 6xch

X-ray diffraction
2.2Å resolution

Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Leupeptin

Released:
DOI: 10.2210/pdb6xch/pdb
PDB entry 6xch coloured by chain, front view.
PDB entry 6xch coloured by chain, side view.
PDB entry 6xch coloured by chain, top view.
Source organisms:
Primary publication:
Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals.
Kneller DW, Galanie S, Phillips G, O'Neill HM, Coates L, Kovalevsky A
Structure 28 1313-1320.e3 (2020)
PMID: 33152262

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + a 5'-(5'-triphosphoguanosine)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA]
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145090 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
3C-like proteinase nsp5 Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.83 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus endopeptidase C30
Leupeptin Chain: C
Molecule details ›
Chain: C
Length: 4 amino acids
Theoretical weight: 430 Da
Source organism: Streptomyces exfoliatus
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Unit cell:
a: 46.586Å b: 53.307Å c: 113.275Å
α: 90° β: 101° γ: 90°
R-values:
R R work R free
0.199 0.197 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Structural biology of SARS-CoV-2 and implications for therapeutic development.
Yang et al. (2021)
14 more

12 mentions without citation

Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be.
Mariano et al. (2020)
11 more